CRAN Package Check Results for Package outbreaker

Last updated on 2015-09-02 06:48:07.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-5 6.39 53.54 59.93 ERROR
r-devel-linux-x86_64-debian-gcc 1.1-5 6.39 49.88 56.28 ERROR
r-devel-windows-ix86+x86_64 1.1-5 49.00 124.00 173.00 ERROR
r-patched-linux-x86_64 1.1-5 6.84 52.76 59.60 ERROR
r-release-linux-x86_64 1.1-5 6.66 53.80 60.46 ERROR
r-release-osx-x86_64-mavericks 1.1-5 OK
r-oldrel-windows-ix86+x86_64 1.1-5 58.00 270.00 328.00 ERROR

Check Details

Version: 1.1-5
Check: R code for possible problems
Result: NOTE
    .kernel.expo: no visible global function definition for ‘dist’
    .kernel.expo: no visible global function definition for ‘dexp’
    .plot.kernel.expo: no visible global function definition for ‘plot’
    .plot.kernel.expo : <anonymous>: no visible global function definition
     for ‘dexp’
    as.igraph.simOutbreak : edge.col.pal: no visible global function
     definition for ‘grey’
    as.igraph.tTree : col.pal: no visible global function definition for
     ‘grey’
    disperse: no visible global function definition for ‘rnorm’
    get.Rt: no visible global function definition for ‘boxplot’
    get.Rt: no visible global function definition for ‘matplot’
    get.incid: no visible global function definition for ‘boxplot’
    get.incid: no visible global function definition for ‘matplot’
    get.tTree: no visible binding for global variable ‘median’
    outbreaker: no visible global function definition for ‘runif’
    outbreaker: no visible global function definition for ‘read.table’
    outbreaker.parallel: no visible global function definition for ‘runif’
    plot.simOutbreak: no visible global function definition for ‘plot’
    plot.tTree: no visible global function definition for ‘plot’
    plotChains: no visible global function definition for ‘matplot’
    plotChains: no visible binding for global variable ‘density’
    plotChains: no visible global function definition for ‘density’
    plotChains: no visible global function definition for ‘plot’
    plotChains : <anonymous>: no visible global function definition for
     ‘lines’
    plotOutbreak: no visible global function definition for
     ‘colorRampPalette’
    plotOutbreak: no visible global function definition for ‘boxplot’
    plotOutbreak : <anonymous>: no visible global function definition for
     ‘points’
    plotOutbreak: no visible global function definition for ‘points’
    plotOutbreak : edge.col.pal: no visible global function definition for
     ‘grey’
    plotOutbreak : drawArrow: no visible global function definition for
     ‘arrows’
    plotOutbreak : drawArrow: no visible global function definition for
     ‘text’
    selectChains: no visible global function definition for ‘anova’
    selectChains: no visible global function definition for ‘lm’
    simOutbreak : seq.dupli: no visible global function definition for
     ‘rbinom’
    simOutbreak: no visible global function definition for ‘runif’
    simOutbreak: no visible global function definition for ‘rbinom’
    simOutbreak: no visible global function definition for ‘rpois’
    transGraph : col.pal: no visible global function definition for ‘grey’
    transGraph: no visible global function definition for ‘plot’
    Undefined global functions or variables:
     anova arrows boxplot colorRampPalette density dexp dist grey lines lm
     matplot median plot points rbinom read.table rnorm rpois runif text
    Consider adding
     importFrom("grDevices", "colorRampPalette", "grey")
     importFrom("graphics", "arrows", "boxplot", "lines", "matplot", "plot",
     "points", "text")
     importFrom("stats", "anova", "density", "dexp", "dist", "lm", "median",
     "rbinom", "rnorm", "rpois", "runif")
     importFrom("utils", "read.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 1.1-5
Check: examples
Result: ERROR
    Running examples in ‘outbreaker-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: simulated outbreak dataset
    > ### Title: Toy outbreak dataset used to illustrate outbreaker
    > ### Aliases: fakeOutbreak
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D ## COMMAND LINES TO GENERATE SIMILAR DATA ##
    > ##D w <- c(0, 0.5, 1, 0.75)
    > ##D ## note: this works only if outbreak has at least 30 case
    > ##D dat <- simOutbreak(R0 = 2, infec.curve = w, n.hosts = 100)[1:30]
    > ##D collecDates <- dat$onset + sample(0:3, size=30, replace=TRUE, prob=w)
    > ## End(Not run)
    >
    > ## EXAMPLE USING TOYOUTBREAK ##
    > ## LOAD DATA, SET RANDOM SEED
    > data(fakeOutbreak)
    > attach(fakeOutbreak)
    >
    > ## VISUALIZE DYNAMICS
    > matplot(dat$dynam, type="o", pch=20, lty=1,
    + main="Outbreak dynamics", xlim=c(0,28))
    > legend("topright", legend=c("S","I","R"), lty=1, col=1:3)
    >
    > ## VISUALIZE TRANSMISSION TREE
    > plot(dat, annot="dist", main="Data - transmission tree")
    > mtext(side=3, "arrow annotations are numbers of mutations")
    >
    >
    > ## Not run:
    > ##D ## RUN OUTBREAKER - PARALLEL VERSION
    > ##D ## (takes < 1 min))
    > ##D set.seed(1)
    > ##D res <- outbreaker.parallel(n.runs=4, dna=dat$dna,
    > ##D dates=collecDates,w.dens=w, n.iter=5e4)
    > ## End(Not run)
    >
    >
    > ## ASSESS CONVERGENCE OF CHAINS
    > plotChains(res)
    > plotChains(res, burnin=2e4)
    >
    > ## REPRESENT POSTERIOR ANCESTRIES
    > transGraph(res, annot="", main="Posterior ancestries", thres=.01)
    Error in layout_with_fr(list(30, TRUE, c(0, 1, 2, 3, 3, 4, 5, 5, 6, 4, :
     unused argument (rescale = FALSE)
    Calls: transGraph ... layout.fruchterman.reingold -> do_call -> eval -> eval -> layout_with_fr
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1-5
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'outbreaker-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: simulated outbreak dataset
    > ### Title: Toy outbreak dataset used to illustrate outbreaker
    > ### Aliases: fakeOutbreak
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D ## COMMAND LINES TO GENERATE SIMILAR DATA ##
    > ##D w <- c(0, 0.5, 1, 0.75)
    > ##D ## note: this works only if outbreak has at least 30 case
    > ##D dat <- simOutbreak(R0 = 2, infec.curve = w, n.hosts = 100)[1:30]
    > ##D collecDates <- dat$onset + sample(0:3, size=30, replace=TRUE, prob=w)
    > ## End(Not run)
    >
    > ## EXAMPLE USING TOYOUTBREAK ##
    > ## LOAD DATA, SET RANDOM SEED
    > data(fakeOutbreak)
    > attach(fakeOutbreak)
    >
    > ## VISUALIZE DYNAMICS
    > matplot(dat$dynam, type="o", pch=20, lty=1,
    + main="Outbreak dynamics", xlim=c(0,28))
    > legend("topright", legend=c("S","I","R"), lty=1, col=1:3)
    >
    > ## VISUALIZE TRANSMISSION TREE
    > plot(dat, annot="dist", main="Data - transmission tree")
    > mtext(side=3, "arrow annotations are numbers of mutations")
    >
    >
    > ## Not run:
    > ##D ## RUN OUTBREAKER - PARALLEL VERSION
    > ##D ## (takes < 1 min))
    > ##D set.seed(1)
    > ##D res <- outbreaker.parallel(n.runs=4, dna=dat$dna,
    > ##D dates=collecDates,w.dens=w, n.iter=5e4)
    > ## End(Not run)
    >
    >
    > ## ASSESS CONVERGENCE OF CHAINS
    > plotChains(res)
    > plotChains(res, burnin=2e4)
    >
    > ## REPRESENT POSTERIOR ANCESTRIES
    > transGraph(res, annot="", main="Posterior ancestries", thres=.01)
    Error in layout_with_fr(list(30, TRUE, c(0, 1, 2, 3, 3, 4, 5, 5, 6, 4, :
     unused argument (rescale = FALSE)
    Calls: transGraph ... layout.fruchterman.reingold -> do_call -> eval -> eval -> layout_with_fr
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-5
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'outbreaker-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: simulated outbreak dataset
    > ### Title: Toy outbreak dataset used to illustrate outbreaker
    > ### Aliases: fakeOutbreak
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D ## COMMAND LINES TO GENERATE SIMILAR DATA ##
    > ##D w <- c(0, 0.5, 1, 0.75)
    > ##D ## note: this works only if outbreak has at least 30 case
    > ##D dat <- simOutbreak(R0 = 2, infec.curve = w, n.hosts = 100)[1:30]
    > ##D collecDates <- dat$onset + sample(0:3, size=30, replace=TRUE, prob=w)
    > ## End(Not run)
    >
    > ## EXAMPLE USING TOYOUTBREAK ##
    > ## LOAD DATA, SET RANDOM SEED
    > data(fakeOutbreak)
    > attach(fakeOutbreak)
    >
    > ## VISUALIZE DYNAMICS
    > matplot(dat$dynam, type="o", pch=20, lty=1,
    + main="Outbreak dynamics", xlim=c(0,28))
    > legend("topright", legend=c("S","I","R"), lty=1, col=1:3)
    >
    > ## VISUALIZE TRANSMISSION TREE
    > plot(dat, annot="dist", main="Data - transmission tree")
    > mtext(side=3, "arrow annotations are numbers of mutations")
    >
    >
    > ## Not run:
    > ##D ## RUN OUTBREAKER - PARALLEL VERSION
    > ##D ## (takes < 1 min))
    > ##D set.seed(1)
    > ##D res <- outbreaker.parallel(n.runs=4, dna=dat$dna,
    > ##D dates=collecDates,w.dens=w, n.iter=5e4)
    > ## End(Not run)
    >
    >
    > ## ASSESS CONVERGENCE OF CHAINS
    > plotChains(res)
    > plotChains(res, burnin=2e4)
    >
    > ## REPRESENT POSTERIOR ANCESTRIES
    > transGraph(res, annot="", main="Posterior ancestries", thres=.01)
    Error in layout_with_fr(list(30, TRUE, c(0, 1, 2, 3, 3, 4, 5, 5, 6, 4, :
     unused argument (rescale = FALSE)
    Calls: transGraph ... layout.fruchterman.reingold -> do_call -> eval -> eval -> layout_with_fr
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64